Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study

Therapeutic Approach Targeting Gut Microbiome in Gastrointestinal Infectious Diseases

While emerging evidence highlights the significance of gut microbiome in gastrointestinal infectious diseases, treatments like Fecal Microbiota Transplantation (FMT) and probiotics are gaining popularity, especially for diarrhea patients. However, the specific role of the gut microbiome in different gastrointestinal infectious diseases remains uncertain. There is no consensus on whether gut modulation therapy is universally effective for all such infections. In this comprehensive review, we examine recent developments of the gut microbiome's involvement in several gastrointestinal infectious diseases, including infection of Helicobacter pylori, Clostridium difficile, Vibrio cholerae, enteric viruses, Salmonella enterica serovar Typhimurium, Pseudomonas aeruginosa Staphylococcus aureus, Candida albicans, and Giardia duodenalis. We have also incorporated information about fungi and engineered bacteria in gastrointestinal infectious diseases, aiming for a more comprehensive overview of the role of the gut microbiome. This review will provide insights into the pathogenic mechanisms of the gut microbiome while exploring the microbiome's potential in the prevention, diagnosis, prediction, and treatment of gastrointestinal infections.

Predicting Vibrio cholerae infection and symptomatic disease: a systems serology study

BACKGROUND

Vibriocidal antibodies are currently the best characterised correlate of protection against cholera and are used to gauge immunogenicity in vaccine trials. Although other circulating antibody responses have been associated with a decreased risk of infection, the correlates of protection against cholera have not been comprehensively compared. We aimed to analyse antibody-mediated correlates of protection from both V cholerae infection and cholera-related diarrhoea.

METHODS

We conducted a systems serology study that analysed 58 serum antibody biomarkers as correlates of protection against V cholerae O1 infection or diarrhoea. We used serum samples from two cohorts: household contacts of people with confirmed cholera in Dhaka, Bangladesh, and cholera-naive volunteers who were recruited at three centres in the USA, vaccinated with a single dose of CVD 103-HgR live oral cholera vaccine, and then challenged with V cholerae O1 El Tor Inaba strain N16961. We measured antigen-specific immunoglobulin responses against antigens using a customised Luminex assay and used conditional random forest models to examine which baseline biomarkers were most important for classifying individuals who went on to develop infection versus those who remained uninfected or asymptomatic. V cholerae infection was defined as having a positive stool culture result on days 2-7 or day 30 after enrolment of the household's index cholera case and, in the vaccine challenge cohort, was the development of symptomatic diarrhoea (defined as two or more loose stools of ≥200 mL each, or a single loose stool of ≥300 mL over a 48-h period).

FINDINGS

In the household contact cohort (261 participants from 180 households), 20 (34%) of the 58 studied biomarkers were associated with protection against V cholerae infection. We identified serum antibody-dependent complement deposition targeting the O1 antigen as the most predictive correlate of protection from infection in the household contacts, whereas vibriocidal antibody titres ranked lower. A five-biomarker model predicted protection from V cholerae infection with a cross-validated area under the curve (cvAUC) of 79% (95% CI 73-85). This model also predicted protection against diarrhoea in unvaccinated volunteers challenged with V cholerae O1 after vaccination (n=67; area under the curve [AUC] 77%, 95% CI 64-90). Although a different five-biomarker model best predicted protection from the development of cholera diarrhoea in the challenged vaccinees (cvAUC 78%, 95% CI 66-91), this model did poorly at predicting protection against infection in the household contacts (AUC 60%, 52-67).

INTERPRETATION

Several biomarkers predict protection better than vibriocidal titres. A model based on protection against infection among household contacts was predictive of protection against both infection and diarrhoeal illness in challenged vaccinees, suggesting that models based on observed conditions in a cholera-endemic population might be more likely to identify broadly applicable correlates of protection than models trained on single experimental settings.

FUNDING

National Institute of Allergy and Infectious Diseases and National Institute of Child Health and Human Development, National Institutes of Health.

Immune evasion and persistence in enteric bacterial pathogens

The major function of the mammalian immune system is to prevent and control infections caused by enteropathogens that collectively have altered human destiny. In fact, as the gastrointestinal tissues are the major interface of mammals with the environment, up to 70% of the human immune system is dedicated to patrolling them The defenses are multi-tiered and include the endogenous microflora that mediate colonization resistance as well as physical barriers intended to compartmentalize infections. The gastrointestinal tract and associated lymphoid tissue are also protected by sophisticated interleaved arrays of active innate and adaptive immune defenses. Remarkably, some bacterial enteropathogens have acquired an arsenal of virulence factors with which they neutralize all these formidable barriers to infection, causing disease ranging from mild self-limiting gastroenteritis to in some cases devastating human disease.

Intestinal colonization against Vibrio cholerae: host and microbial resistance mechanisms

Vibrio cholerae is a non-invasive enteric pathogen known to cause a major public health problem called cholera. The pathogen inhabits the aquatic environment while outside the human host, it is transmitted into the host easily through ingesting contaminated food and water containing the vibrios, thus causing diarrhoea and vomiting. V. cholerae must resist several layers of colonization resistance mechanisms derived from the host or the gut commensals to successfully survive, grow, and colonize the distal intestinal epithelium, thus causing an infection. The colonization resistance mechanisms derived from the host are not specific to V. cholerae but to all invading pathogens. However, some of the gut commensal-derived colonization resistance may be more specific to the pathogen, making it more challenging to overcome. Consequently, the pathogen has evolved well-coordinated mechanisms that sense and utilize the anti-colonization factors to modulate events that promote its survival and colonization in the gut. This review is aimed at discussing how V. cholerae interacts and resists both host- and microbe-specific colonization resistance mechanisms to cause infection.

Mucosal and systemic immune responses to Vibrio cholerae infection and oral cholera vaccines (OCVs) in humans: a systematic review

INTRODUCTION

Cholera is an enteric disease caused by Vibrio cholerae, a water-borne pathogen, and characterized by severe diarrhea. Vaccines have been recommended for use by the WHO in resource-limited settings. Efficacies of the currently licensed cholera vaccines are not optimal in endemic settings and low in children below the age of five, a section of the population most susceptible to the disease. Development of next generation of cholera vaccines would require a detailed understanding of the required protective immune responses.

AREA COVERED

In this review, we revisit clinical trials which are focused on the early transcriptional mucosal responses elicited during Vibrio cholerae infection and upon vaccination along with summarizing various components of the effector immune response against Vibrio cholerae.

EXPERT OPINION

The inability of currently licensed killed/inactivated vaccines to elicit key inflammatory pathways locally may explain their restricted efficacy in endemic settings. More studies are required to understand the immunogenicity of the live attenuated cholera vaccine in these regions. Various extrinsic and intrinsic factors influence anti-cholera immunity and need to be considered to develop region-specific next generation vaccines.

Random forest model can predict the prognosis of hospital-acquired Klebsiella pneumoniae infection as well as traditional logistic regression model

OBJECTIVE

To explore if random forest (RF) model can predict the prognosis of hospital-acquired Klebsiella pneumoniae infection as well as traditional logistic regression(LR) model.

METHODS

A total of 254 cases of hospital-acquired Klebsiella pneumoniae infection in a tertiary hospital in Beijing from January 2016 to December 2020 were retrospectively collected. Appropriate influencing factors were selected by referring to relevant articles from the aspects of basic clinical information and contact history before infection, and divided into a training set and a test set. Both the RF and LR models were trained by the training set, and using testing set to compare these two models.

RESULTS

The prediction accuracy of the LR model was 87.0%, the true positive rate of the LR model was 94.7%; the false negative rate of the LR model was 5.3%; the false positive rate of the LR model was 35%; the true negative rate of the LR model was 65%; the sensitivity of the LR model for the prognosis prediction of hospital-acquired Klebsiella pneumoniae infection was 94.7%; and the specificity was 65%. The prediction accuracy of the RF model was 89.6%; the true positive rate of the RF model was 92.1%; the false negative rate of the RF model was 7.9%; the false positive rate of the RF model was 21.4%; the true negative rate of the RF model was 78.6%; the sensitivity of the RF model for the prognosis prediction of hospital-acquired Klebsiella pneumoniae infection was 92.1%; and the specificity was 78.6%. ROC curve shows that the area under curve(AUC) of the LR model was 0.91, and that of the RF model was 0.95.

CONCLUSION

The RF model has higher specificity, sensitivity, and accuracy for the prognostic prediction of hospital-acquired Klebsiella pneumoniae infection than the LR model and has greater clinical application prospects.

Cholera

Cholera was first described in the areas around the Bay of Bengal and spread globally, resulting in seven pandemics during the past two centuries. It is caused by toxigenic Vibrio cholerae O1 or O139 bacteria. Cholera is characterised by mild to potentially fatal acute watery diarrhoeal disease. Prompt rehydration therapy is the cornerstone of management. We present an overview of cholera and its pathogenesis, natural history, bacteriology, and epidemiology, while highlighting advances over the past 10 years in molecular epidemiology, immunology, and vaccine development and deployment. Since 2014, the Global Task Force on Cholera Control, a WHO coordinated network of partners, has been working with several countries to develop national cholera control strategies. The global roadmap for cholera control focuses on stopping transmission in cholera hotspots through vaccination and improved water, sanitation, and hygiene, with the aim to reduce cholera deaths by 90% and eliminate local transmission in at least 20 countries by 2030.

Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement

Recent studies indicate that the human intestinal microbiota could impact the outcome of infection by Vibrio cholerae, the etiological agent of the diarrheal disease cholera. A commensal bacterium, Paracoccus aminovorans, was previously identified in high abundance in stool collected from individuals infected with V. cholerae when compared to stool from uninfected persons. However, if and how P. aminovorans interacts with V. cholerae has not been experimentally determined; moreover, whether any association between this bacterium alters the behaviors of V. cholerae to affect the disease outcome is unclear. Here, we show that P. aminovorans and V. cholerae together form dual-species biofilm structure at the air–liquid interface, with previously uncharacterized novel features. Importantly, the presence of P. aminovorans within the murine small intestine enhances V. cholerae colonization in the same niche that is dependent on the Vibrio exopolysaccharide and other major components of mature V. cholerae biofilm. These studies illustrate that multispecies biofilm formation is a plausible mechanism used by a gut microbe to increase the virulence of the pathogen, and this interaction may alter outcomes in enteric infections.

A commensal-encoded genotoxin drives restriction of Vibrio cholerae colonization and host gut microbiome remodeling

SignificanceIn a polymicrobial battlefield where different species compete for nutrients and colonization niches, antimicrobial compounds are the sword and shield of commensal microbes in competition with invading pathogens and each other. The identification of an Escherichia coli-produced genotoxin, colibactin, and its specific targeted killing of enteric pathogens and commensals, including Vibrio cholerae and Bacteroides fragilis, sheds light on our understanding of intermicrobial interactions in the mammalian gut. Our findings elucidate the mechanisms through which genotoxins shape microbial communities and provide a platform for probing the larger role of enteric multibacterial interactions regarding infection and disease outcomes.

Animal models for dissecting Vibrio cholerae intestinal pathogenesis and immunity

The human diarrheal disease cholera is caused by the bacterium Vibrio cholerae. Efforts to develop animal models that closely mimic cholera to study the pathogenesis of this disease began >125 years ago. Here, we review currently used non-surgical, oral inoculation-based animal models for investigation of V. cholerae intestinal colonization and disease and highlight recent discoveries that have illuminated mechanisms of cholera pathogenesis and immunity, particularly in the area of how V. cholerae interacts with the gut microbiome to influence infection. The emergence of high-throughput tools for studies of pathogen-host interactions, along with continued advances in host genetic engineering and manipulation in animal models of V. cholerae will deepen understanding of cholera pathogenesis, uncovering knowledge important for control of this globally important bacterial pathogen.

Systemic, Mucosal, and Memory Immune Responses following Cholera

Vibrio cholerae O1, the major causative agent of cholera, remains a significant public health threat. Although there are available vaccines for cholera, the protection provided by killed whole-cell cholera vaccines in young children is poor. An obstacle to the development of improved cholera vaccines is the need for a better understanding of the primary mechanisms of cholera immunity and identification of improved correlates of protection. Considerable progress has been made over the last decade in understanding the adaptive and innate immune responses to cholera disease as well as V. cholerae infection. This review will assess what is currently known about the systemic, mucosal, memory, and innate immune responses to clinical cholera, as well as recent advances in our understanding of the mechanisms and correlates of protection against V. cholerae O1 infection.

A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients

Vibrio cholerae can cause a range of symptoms, from severe diarrhea to asymptomatic infection. Previous studies using whole-genome sequencing (WGS) of multiple bacterial isolates per patient showed that V. cholerae can evolve modest genetic diversity during symptomatic infection. To further explore the extent of V. cholerae within-host diversity, we applied culture-based WGS and metagenomics to a cohort of both symptomatic and asymptomatic cholera patients from Bangladesh. While metagenomics allowed us to detect more mutations in symptomatic patients, WGS of cultured isolates was necessary to detect V. cholerae diversity in asymptomatic carriers, likely due to their low V. cholerae load. Using both metagenomics and isolate WGS, we report three lines of evidence that V. cholerae hypermutators evolve within patients. First, we identified nonsynonymous mutations in V. cholerae DNA repair genes in 5 out of 11 patient metagenomes sequenced with sufficient coverage of the V. cholerae genome and in 1 of 3 patients with isolate genomes sequenced. Second, these mutations in DNA repair genes tended to be accompanied by an excess of intrahost single nucleotide variants (iSNVs). Third, these iSNVs were enriched in transversion mutations, a known hallmark of hypermutator phenotypes. While hypermutators appeared to generate mostly selectively neutral mutations, nonmutators showed signs of convergent mutation across multiple patients, suggesting V. cholerae adaptation within hosts. Our results highlight the power and limitations of metagenomics combined with isolate sequencing to characterize within-patient diversity in acute V. cholerae infections, while providing evidence for hypermutator phenotypes within cholera patients.

IMPORTANCE Pathogen evolution within patients can impact phenotypes such as drug resistance and virulence, potentially affecting clinical outcomes. V. cholerae infection can result in life-threatening diarrheal disease or asymptomatic infection. Here, we describe whole-genome sequencing of V. cholerae isolates and culture-free metagenomic sequencing from stool of symptomatic cholera patients and asymptomatic carriers. Despite the typically short duration of cholera, we found evidence for adaptive mutations in the V. cholerae genome that occur independently and repeatedly within multiple symptomatic patients. We also identified V. cholerae hypermutator phenotypes within several patients, which appear to generate mainly neutral or deleterious mutations. Our work sets the stage for future studies of the role of hypermutators and within-patient evolution in explaining the variation from asymptomatic carriage to symptomatic cholera.

Environmental parameters associated with incidence and transmission of pathogenic Vibrio spp

Vibrio spp. thrive in warm water and moderate salinity, and they are associated with aquatic invertebrates, notably crustaceans and zooplankton. At least 12 Vibrio spp. are known to cause infection in humans, and Vibrio cholerae is well documented as the etiological agent of pandemic cholera. Pathogenic non-cholera Vibrio spp., e.g., Vibrio parahaemolyticus and Vibrio vulnificus, cause gastroenteritis, septicemia, and other extra-intestinal infections. Incidence of vibriosis is rising globally, with evidence that anthropogenic factors, primarily emissions of carbon dioxide associated with atmospheric warming and more frequent and intense heatwaves, significantly influence environmental parameters, e.g., temperature, salinity, and nutrients, all of which can enhance growth of Vibrio spp. in aquatic ecosystems. It is not possible to eliminate Vibrio spp., as they are autochthonous to the aquatic environment and many play a critical role in carbon and nitrogen cycling. Risk prediction models provide an early warning that is essential for safeguarding public health. This is especially important for regions of the world vulnerable to infrastructure instability, including lack of 'water, sanitation, and hygiene' (WASH), and a less resilient infrastructure that is vulnerable to natural calamity, e.g., hurricanes, floods, and earthquakes, and/or social disruption and civil unrest, arising from war, coups, political crisis, and economic recession. Incorporating environmental, social, and behavioural parameters into such models allows improved prediction, particularly of cholera epidemics. We have reported that damage to WASH infrastructure, coupled with elevated air temperatures and followed by above average rainfall, promotes exposure of a population to contaminated water and increases the risk of an outbreak of cholera. Interestingly, global predictive risk models successful for cholera have the potential, with modification, to predict diseases caused by other clinically relevant Vibrio spp. In the research reported here, the focus was on environmental parameters associated with incidence and distribution of clinically relevant Vibrio spp. and their role in disease transmission. In addition, molecular methods designed for detection and enumeration proved useful for predictive modelling and are described, namely in the context of prediction of environmental conditions favourable to Vibrio spp., hence human health risk.

Dissecting serotype-specific contributions to live oral cholera vaccine efficacy

The O1 serogroup of Vibrio cholerae causes pandemic cholera and is divided into the Ogawa and Inaba serotypes. The O-antigen is V. cholerae's immunodominant antigen, and the two serotypes, which differ by the presence or absence of a terminally methylated O-antigen, likely influence development of immunity to cholera and oral cholera vaccines (OCVs). However, there is no consensus regarding the relative immunological potency of each serotype, in part because previous studies relied on genetically heterogeneous strains. Here, we engineered matched serotype variants of a live OCV candidate, HaitiV, and used a germfree mouse model to evaluate the immunogenicity and protective efficacy of each vaccine serotype. By combining vibriocidal antibody quantification with single- and mixed-strain infection assays, we found that all three HaitiV variants-Inaba^V, Ogawa^V, and Hiko^V (bivalent Inaba/Ogawa)-were immunogenic and protective. None of the vaccine serotypes were superior across both of these vaccine metrics, suggesting that the impact of O1-serotype variation in OCV design, although detectable, is subtle. However, all three live vaccines significantly outperformed formalin-killed Hiko^V, supporting the idea that live OCV usage will bolster current cholera control practices. The potency of OCVs was found to be challenge strain-dependent, emphasizing the importance of appropriate strain selection for cholera challenge studies. Our findings and experimental approaches will be valuable for guiding the development of live OCVs and oral vaccines for additional pathogens.

Update on Environmental and Host Factors Impacting the Risk of Vibrio cholerae Infection

Vibrio cholerae is the causative agent of cholera, a diarrheal disease that kills tens of thousands of people each year. Cholera is transmitted primarily by the ingestion of drinking water contaminated with fecal matter, and a safe water supply remains out of reach in many areas of the world. In this Review, we discuss host and environmental factors that impact the susceptibility to V. cholerae infection and the severity of disease.

The Interface of Vibrio cholerae and the Gut Microbiome

The bacterium Vibrio cholerae is the etiologic agent of the severe human diarrheal disease cholera. The gut microbiome, or the native community of microorganisms found in the human gastrointestinal tract, is increasingly being recognized as a factor in driving susceptibility to infection, in vivo fitness, and host interactions of this pathogen. Here, we review a subset of the emerging studies in how gut microbiome structure and microbial function are able to drive V. cholerae virulence gene regulation, metabolism, and modulate host immune responses to cholera infection and vaccination. Improved mechanistic understanding of commensal-pathogen interactions offers new perspectives in the design of prophylactic and therapeutic approaches for cholera control.